SOFTWARE FOR MOLECULAR DYNAMICS SIMULATION ON A PC-BASED PROCESSOR

THIS RESEARCH LEADS TO A PC-BASED MOLECULAR MECHANICS SOFTWARE PACKAGE THAT EXECUTES THE MOST COMPUTE-INTENSIVE SIMULATION AND MINIMALIZATION FUNCTIONS IN PARALLEL ON THE APX MASSIVELY-PARALLEL PROCESSOR. IT WILL BE POSSIBLE TO LINK THIS SOFTWARE PACKAGE WITH A PC VERSION OF THE AMBER MOLECULAR MECHANICS AND DYNAMICS SOFTWARE SYSTEM, REPLACING THE CORRESPONDING AMBER SUBROUTINES. THE RESULT WILL BE A TOOL WITH THE CONFORMATIONAL ANALYSIS CAPABILITIES OF AMBER, A COST WITHIN THE CAPITAL BUDGET OF AN INDIVIDUAL RESEARCHER, LOCAL, DESKTOP COMPUTING, AVOIDING THE DELAYS OF REMOTE JOBS, AND PERFORMANCE APPROACHING THAT OF CONVEX AND CRAY SYSTEMS\APPROACHING INTERACTIVE RESPONSE TIMES, EVEN FOR LARGE SIMULATIONS. IN THE FUTURE, THIS SOFTWARE PACKAGE CAN BE ADAPTED TO LINK WITH OTHER MOLECULAR MECHANICS AND GRAPHICS DISPLAY PROGRAMS. PHASE I RESULTS WILL BE A BASELINE VERSION OF AMBER THAT EXECUTES ON A 386 OR 486 PC, A PC VERSION OF AMBER THAT CONTAINS AT LEAST ONE APX-ACCELERATED FUNCTION, A REPORT SUMMARIZING THE PC/APX-RELATED DESIGN ISSUES, THEIR SOLUTION AND A DEVELOPMENT PLAN FOR PHASE II.